GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Caldicellulosiruptor hydrothermalis 108

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate WP_013403278.1 CALHY_RS07050 pyrroline-5-carboxylate reductase

Query= curated2:O66553
         (265 letters)



>NCBI__GCF_000166355.1:WP_013403278.1
          Length = 260

 Score =  169 bits (427), Expect = 7e-47
 Identities = 93/260 (35%), Positives = 154/260 (59%), Gaps = 3/260 (1%)

Query: 8   MRVGIVGFGNMGQAFALCFSKKLGKENIIVTDKVQEKRNLATEMGIAFASDVKFLADNSD 67
           M++GI+G GNM  + A    + +  +       + +    +   G    +      ++S 
Sbjct: 1   MKIGIIGCGNMASSIAHSIKQSIEAQLFCYDIDIDKANRFSQVYGATKMNSEIETVESSS 60

Query: 68  VVLVAVKPKDSQEVLQKLKD--YKGIILSIMAGVSIEKMEKILGKDKKIVRVMPNVNVAV 125
           ++++AVKPKD  +VL+K+KD   + II+SI AG+SI K+++++G DKKIVRVMPN+N++V
Sbjct: 61  IIIIAVKPKDIFDVLEKIKDGISEKIIVSIAAGISISKIKEVVG-DKKIVRVMPNINISV 119

Query: 126 GSGVMAITDNGNLSEEERSKVEELLLSCGTLYRIEERLFDAFTALAGSGPAFVFSFIDAL 185
             GVM I  +  ++ +E+ K+  L  S G +   +E+  DA TAL GSGPAFV  FI++ 
Sbjct: 120 QKGVMGICFSETVAADEKEKILNLFKSMGEVIATDEKHMDAITALFGSGPAFVAHFIESC 179

Query: 186 ALAGVHQGFSYEQALRIALDTVMGSAKLLKEFQVNPNELIAKVTSPGGTTIEGIKYLEEK 245
             A V  GFS +++L++ L    G+   +K   +   ++   VTSPGGTTIEG+   E +
Sbjct: 180 VDAAVKLGFSRQESLKLILALFEGTVVNMKNNMLTTQQIKDMVTSPGGTTIEGLVEFERR 239

Query: 246 GFKGTVMECINRTSQKAKKL 265
             KG +++ I +  ++AK +
Sbjct: 240 AVKGAIIDGILKAFERAKNI 259


Lambda     K      H
   0.318    0.135    0.368 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 203
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 265
Length of database: 260
Length adjustment: 25
Effective length of query: 240
Effective length of database: 235
Effective search space:    56400
Effective search space used:    56400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_013403278.1 CALHY_RS07050 (pyrroline-5-carboxylate reductase)
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00112.hmm
# target sequence database:        /tmp/gapView.3179937.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00112  [M=263]
Accession:   TIGR00112
Description: proC: pyrroline-5-carboxylate reductase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    7.4e-79  251.1   4.6    8.3e-79  250.9   4.6    1.0  1  NCBI__GCF_000166355.1:WP_013403278.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013403278.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.9   4.6   8.3e-79   8.3e-79       1     262 [.       3     258 ..       3     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 250.9 bits;  conditional E-value: 8.3e-79
                             TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 
                                           i+iiG+Gnm++++++++ ++    ++++  ++   +k++++ + +g++ ++++ e v+ ++++++avKP+d+ 
  NCBI__GCF_000166355.1:WP_013403278.1   3 IGIIGCGNMASSIAHSIKQS---IEAQLFCYDIDIDKANRFSQVYGATKMNSEIETVESSSIIIIAVKPKDIF 72 
                                           89**************9987...35689999999*************************************** PP

                             TIGR00112  74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146
                                           +vl+++k+   + ek+++Si+AG++i+k+++ ++ +k++vRvmPN++ +v++gv++i+ s++v +++ke++ +
  NCBI__GCF_000166355.1:WP_013403278.1  73 DVLEKIKD--GISEKIIVSIAAGISISKIKEVVG-DKKIVRVMPNINISVQKGVMGICFSETVAADEKEKILN 142
                                           ****9887..7789*******************7.689*********************************** PP

                             TIGR00112 147 llkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehp 219
                                           l+k++G+v+  +ek++da+tal GSgPAfv+++ie+ +da+vklG++r+e+++l+ ++++G++  +++++ + 
  NCBI__GCF_000166355.1:WP_013403278.1 143 LFKSMGEVIATDEKHMDAITALFGSGPAFVAHFIESCVDAAVKLGFSRQESLKLILALFEGTVVNMKNNMLTT 215
                                           ************************************************************************* PP

                             TIGR00112 220 alLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrsee 262
                                           +++kd VtsPgGtTi+gl ++e+ +v++a+i+++ +a +r+++
  NCBI__GCF_000166355.1:WP_013403278.1 216 QQIKDMVTSPGGTTIEGLVEFERRAVKGAIIDGILKAFERAKN 258
                                           ****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (260 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.24
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory